EP2784080B1 - Peptide-hinge-free flexible antibody-like molecule - Google Patents

Peptide-hinge-free flexible antibody-like molecule Download PDF

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EP2784080B1
EP2784080B1 EP12844691.1A EP12844691A EP2784080B1 EP 2784080 B1 EP2784080 B1 EP 2784080B1 EP 12844691 A EP12844691 A EP 12844691A EP 2784080 B1 EP2784080 B1 EP 2784080B1
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antibody
molecule
peptide
peg
nonpeptide
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German (de)
English (en)
French (fr)
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EP2784080A4 (en
EP2784080A1 (en
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Daniel J. Capon
Koichi Tanaka
Taka-Aki Sato
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Shimadzu Corp
Biomolecular Holdings LLC
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Shimadzu Corp
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • C07K14/4701—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals not used
    • C07K14/4711—Alzheimer's disease; Amyloid plaque core protein
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K7/00—Peptides having 5 to 20 amino acids in a fully defined sequence; Derivatives thereof
    • C07K7/04—Linear peptides containing only normal peptide links
    • C07K7/06—Linear peptides containing only normal peptide links having 5 to 11 amino acids
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K7/00—Peptides having 5 to 20 amino acids in a fully defined sequence; Derivatives thereof
    • C07K7/04—Linear peptides containing only normal peptide links
    • C07K7/08—Linear peptides containing only normal peptide links having 12 to 20 amino acids
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
    • C07K2317/52—Constant or Fc region; Isotype
    • C07K2317/53—Hinge
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/01—Fusion polypeptide containing a localisation/targetting motif
    • C07K2319/02—Fusion polypeptide containing a localisation/targetting motif containing a signal sequence
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/30—Non-immunoglobulin-derived peptide or protein having an immunoglobulin constant or Fc region, or a fragment thereof, attached thereto

Definitions

  • the present invention relates to an artificial antibody. More specifically, the present invention relates to a flexible antibody-like molecule having a nonpeptide hinge part.
  • Non-Patent Document 1 The essence of an antibody molecule is its Y-shape.
  • Non-Patent Document 1 The essence of an antibody molecule is its Y-shape.
  • Non-Patent Document 1 The sequence of one part (Fc) of these sections was shown to be essentially conserved in all ⁇ -globulins, while the other two sections (Fab) were shown to vary considerably in sequence from molecule to molecule.
  • Non-Patent Document 3 Papain cleavage occurs within two heavy chains so that Fab arms, each of which has a light chain bound to the N-terminal portion of the heavy chain by a disulfide, are released from an Fc fragment that is a disulfide-bound dimer composed of the C-terminal half of the heavy chains. All of the cysteines participating in these interchain disulfide bonds are clustered at the very middle of the heavy chain, giving the ⁇ -globulins their Y-shape.
  • Non-Patent Documents 4 and 5 A more dynamic picture of ⁇ -globulin structure has emerged from electron microscopy of antibody-antigen complexes 4),5) (Non-Patent Documents 4 and 5).
  • antibodies form cyclic dimers, trimers, tetramers, pentamers, and larger structures.
  • the Fab part and the Fc part have the appearance of rigid rods, the angle between them varies from zero to 180°, allowing them to bridge antigens at distances up to 120 angstroms.
  • the antibody behaves as if all the three parts were bound by a "hinge part" that is a name now used for a heavy chain region containing interchain disulfides.
  • Non-Patent Document 6 reveals extreme asymmetry in the placement of the Fab arms, and this reflects differences in their distance and rotational displacement from Fc.
  • the hinge parts on adjacent heavy chains are mutually separated by a distance of 18 angstroms or less, the Fab arms diverge at a 148° angle along their major axes and are rotated by 158° along their depth axes.
  • Non-Patent Documents 7 to 14 Y-shaped antibody-like molecules (called immunoadhesins or Fc fusion proteins) are cleaved by papain, like antibodies, into three fragments and have many of the biological properties of IgG including a long plasma half-life, Fc receptor and complement binding, and the ability to cross the placenta. All of them were shown to have therapeutic potential.
  • immunoadhesins or Fc fusion proteins are cleaved by papain, like antibodies, into three fragments and have many of the biological properties of IgG including a long plasma half-life, Fc receptor and complement binding, and the ability to cross the placenta. All of them were shown to have therapeutic potential.
  • Non-Patent Document 7 etanercept (TNF receptor), abatacept (CTLA-4), alefacept (LFA-3), rilonacept (IL-1 receptor), and romiplostim (thrombopoietin analog) 15) (Non-Patent Document 15).
  • TNF receptor etanercept
  • CTLA-4 abatacept
  • LFA-3 alefacept
  • IL-1 receptor rilonacept
  • romiplostim thrombopoietin analog
  • US2005/027109 discloses an antibody-like molecule comprising a homodimer-forming cysteine-Fc fragment to which a biologically active compound such as polypeptides is coupled either directly or via a linker.
  • US2009/053246 describes a pegylated Fc fragment used as a drug carrier.
  • the Fc fragment is linked to the drug via a linker.
  • US2008/254512 describes hybrid immunoglobulins comprising moving parts linked together via an X-X bond, where X may be a terminal cysteine or selenocysteine.
  • the above-described approved therapeutic antibodies are directed against targets that are multimeric proteins. This suggests that the therapeutic antibodies could be improved if both arms could grasp a particular target molecule.
  • the hinge part normally points the Fab arms away from each other. Outwardly pointing arms may have evolved to grasp large disease targets such as bacteria, but inwardly pointing arms would make it easy to grasp smaller targets such as proteins (e.g., TNF). The latter would likely require that the hinge part is not only flexible but also extendible to a distance of at least several nanometers away from Fc (a combination of properties that are found in many types of polymer chains, but are typically lacking in polypeptides 16) ).
  • the present inventors have devised a chemical synthesis method based on a native chemical ligation 17) that gives quantitative yields of Fc fusion proteins but is appropriate to a native, biologically active Fc molecule.
  • the present inventors will report a novel chemical synthesis method for producing a symmetroadhesin that is an antibody-like molecule having a nonprotein hinge region that is more flexible and extendible and is capable of two-handed binding.
  • the present inventors fused a 15 amino acid peptide having the immunodominant epitope of Alzheimer's A ⁇ (1-42) fibrils 18) to 21) and successfully incorporated nonprotein chains between the A ⁇ and Fc moieties. That is, a native chemical ligation was performed under mild, non-denaturing conditions to bind a ligand binding domain (A ⁇ peptide) to an IgG1 Fc dimer via discrete oxyethylene oligomers of various lengths. Two-handed A ⁇ -Fc fusion proteins were obtained in quantitative yield and shown by surface plasmon resonance to bind to an anti-A ⁇ antibody with a K D that is at least two orders of magnitude smaller than a control A ⁇ peptide.
  • MALDI-TOF MS as developed by Tanaka et al. 22),23
  • MALDI-TOF MS analysis confirmed the protein/nonprotein/protein structure of the two-handed molecule, and this demonstrated that complex protein-nonprotein hybrids were detected by desorption/ionization of peptide sequences contained therein.
  • the present inventors anticipate many applications for symmetroadhesins that combine the target specificity of antibodies with the novel physical, chemical, and biological properties of nonprotein hinge part.
  • the present invention includes the following aspects.
  • the present invention can provide an antibody-like molecule that can bind to a target with higher affinity (specifically, with a smaller dissociation constant K D ).
  • the molecule having at least two hands provided by the present inventors binds to a target with exceptional affinity, and therefore such an improved antibody holds great promise for future development of antibody therapeutics.
  • a flexible antibody-like molecule having a nonpeptide hinge part which comprises a molecular recognition system-forming substance X, an alkyleneoxide group-containing group Y bound to the molecular recognition system-forming substance X, an antibody hinge region-forming sequence bound to the alkyleneoxide-containing group, and an antibody Fc fragment bound to the antibody hinge region-forming sequence.
  • binding includes direct binding and indirect binding.
  • the molecular recognition system-forming substance X may be one of a guest substance (target molecule) and a host substance (molecular recognition substance) that are generally capable of interacting by non-covalent bond with each other, and specifically, may be an amino acid, a peptide, or a polypeptide (including a protein). Particularly, the molecular recognition system-forming substance X may be an amino acid, a peptide composed of 2 to 50 amino acid residues, or a polypeptide. In the present invention, the molecular recognition system-forming substance X is an amino acid or a peptide composed of 2 to 50 amino acid residues.
  • the guest substance examples include various physiological active substances, but the guest substance is preferably a disease-related substance.
  • a specific example of the guest substance includes amyloid ⁇ (peptide chain comprising all or part of a well-known sequence of amyloid ⁇ ). More specifically, the guest substance is a peptide chain having at least the sequence of amyloid ⁇ (3-7), EFRHD (SEQ ID No. 3) that is the epitope of amyloid ⁇ .
  • the peptide chain include a peptide chain having the sequence of amyloid ⁇ (3-7), a peptide chain having the sequence of amyloid ⁇ (1-15), DAEFRHDSGYEVHHQ (SEQ ID No. 2), a peptide chain having the sequence of amyloid ⁇ (1-42), DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA (SEQ ID No. 4), and the like.
  • the host substance may be a substance that is capable of molecular recognition of the target molecule (which may be either a biological molecule or a non-biological molecule).
  • the host substance include an antibody Fab fragment, an aptamer, and the like.
  • molecular recognition means that the molecular recognition site of a molecular recognition substance recognizes and interacts by non-covalent bond with the epitope of a specific target molecule.
  • molecular recognition may be affinity specific binding at an association rate constant ka (unit: 1/Ms) of at least 10 3 or 10 4 , for example, 10 3 to 10 5 or 10 4 to 10 5 .
  • the alkyleneoxide-containing group Y is a bivalent group and may be, for example, a group containing an alkyleneoxide with 2 to 6 carbon atoms. More specifically, the alkyleneoxide in the alkyleneoxide-containing group is ethyleneoxide or propyleneoxide.
  • the alkyleneoxide-containing group is preferably a polyalkyleneoxide-containing group. Therefore, the alkyleneoxide-containing group is preferably a polyalkyleneglycol group formed by polymerization of alkyleneglycol with 2 to 6 carbon atoms (e.g., polymerization degree of 2 to 50).
  • the polyalkyleneglycol group may be selected from the group consisting of a polyethyleneglycol group (a group formed by polymerization of ethyleneglycol) and a polypropyleneglycol group (a group formed by polymerization of 1,2-propanediol or 1,3-propanediol).
  • an ethyleneglycol group or a polyethyleneglycol group with a polymerization degree of 2 to 50, preferably 12 to 36 may be selected.
  • the alkyleneoxide-containing group Y is a polyethyleneglycol group with a polymerization degree of 12 to 36, preferably with a polymerization degree of 12, 24 or 36.
  • the alkyleneoxide-containing group Y imparts flexibility, or flexibility and extendibility to the hinge region of the antibody-like molecule according to the present invention.
  • the antibody examples include IgG1, IgG2, IgG3, IgG4, and the like.
  • the antibody may be one derived from any animal, but is particularly one derived from a human. Further, the antibody may be modified in terms of genetic engineering.
  • Examples of the antibody hinge region-forming sequence include an antibody upper hinge region-forming sequence Z U , an antibody core hinge region-forming sequence Z C , and an antibody lower hinge region-forming sequence Z L , and the antibody-like molecule according to the present invention may contain all these sequences.
  • a core hinge region is a region that is adjacent to the C-terminal side of an upper hinge region and the N-terminal side of a lower hinge region in the hinge region of an antibody, and has at least two cysteine residues forming interchain disulfide bridges between heavy chains.
  • each of the hinge region-forming sequences is part or all of the sequence of each of the hinge regions.
  • the upper hinge region-forming sequence Z U may be part of the sequence of the upper hinge region, for example, a short sequence composed of, for example, 3 to 5 amino acid residues.
  • the upper hinge region-forming sequence Z U is part of the sequence of the IgG1 upper hinge region, DKTHT (SEQ ID No. 1). Further in this case, it is preferred that no cysteine residue is bound to the N-terminal of the sequence DKTHT in the antibody-like molecule according to the present invention.
  • the core hinge region-forming sequence Z C has at least two cysteine residues forming interchain disulfide bridges between heavy chains, and the N terminal-side cysteine residue of the two cysteine residues preferably corresponds to the N-terminal amino acid residue of the core hinge region-forming sequence Z C .
  • One example of the core hinge region-forming sequence Z C is CPPC (SEQ ID No. 5) that is the sequence of the IgG1 core hinge region.
  • antibody lower hinge region-forming sequence Z L is PAELLGGP (SEQ ID No. 6) that is the sequence of the IgG1 antibody lower hinge region.
  • the antibody Fc fragment is a polypeptide forming part or all of an antibody Fc region.
  • the antibody Fc fragment may have the second heavy chain constant region (CH2) and the third heavy chain constant region (CH3).
  • the antibody Fc fragment may comprise a sequence containing of SVFLFPPKPK (SEQ ID No. 7) as at least part.
  • the Fc fragment may be in the form of a dimer or a larger multimer (e.g., up to a decamer). In the present invention, the Fc fragment is in the form of a dimer.
  • the antibody-like molecule according to the present invention has two nonpeptide hinge part-containing groups (XYZ U -groups) each containing the molecular recognition system-forming substance X, the alkyleneoxide-containing group Y, and the antibody upper hinge region-forming sequence Z U .
  • the antibody-like molecule having such a structure may be referred to as a two-handed antibody-like molecule.
  • the Fc fragment in the antibody-like molecule according to the present invention is in the form of a dimer, the antibody-like molecule may have two or more nonpeptide hinge part-containing groups (XYZ U -groups) and therefore may form two or more-handed antibody-like molecule.
  • a counterpart substance of X which forms a molecular recognition system in which the antibody-like molecule according to the present invention can be involved, is determined by those skilled in the art based on the properties of X.
  • the counterpart substance may be a monomeric molecule, a dimer or a larger multimer of molecules, or an aggregate of molecules.
  • the counterpart substance may be either a biological substance or a non-biological substance.
  • the counterpart substance may be a low molecular-weight molecule (e.g., molecular weight of 80,000 or less, or 30,000 or less).
  • the counterpart substance may be a low molecular-weight protein such as cytokine.
  • the association rate constant ka (unit: 1/Ms) of each hand is as described above and is equal to that in a case where the molecular recognition system-forming substance X is a single molecule, but the dissociation rate constant kd (unit: 1/s) is smaller than that in such a case as described above.
  • the dissociation constant K D (unit: M) is smaller than that in such a case as described above, and may be, for example, at most 10 -9 , 10 -10 , 10 -11 , or 10 -12 , for example, 10 -13 to 10 -9 .
  • the antibody-like molecule according to the present invention may be used in any application utilizing a molecular recognition system.
  • examples of such an application include in-vitro diagnostic agents, molecular target drugs, ELISA (Enzyme-Linked ImmunoSorbent Assay) reagents, probes for molecular imaging [PET (positron emission tomography), optical imaging], and the like.
  • PET positron emission tomography
  • Those skilled in the art can select an appropriate molecular recognition system-forming substance X depending on the intended use of the antibody-like molecule.
  • the antibody-like molecule may further contain a functional group (signal group, etc.).
  • the antibody-like molecule according to the present invention is produced in the following manner.
  • a nonpeptide hinge part-containing thioester (XYZ U -COSR) containing a molecular recognition system-forming substance X, an alkyleneoxide-containing group Y, and an antibody upper hinge region-forming sequence Z U is prepared.
  • COSR represents for a thioester group (derivable from a carboxyl group) of the C-terminal amino acid residue of the antibody upper hinge region-forming sequence Z U
  • R represents an organic group (e.g., a linear or branched alkyl group with 1 to 18 carbon atoms, an aryl group with 6 to 18 carbon atoms, an aralkyl group as a combination thereof).
  • the molecular recognition system-forming substance X may be either a biological substance or a non-biological substance, and may be obtained by any method which is well-known to those skilled in the art such as isolation from a natural product, organic chemical synthesis, biochemical production, or semisynthesis.
  • the biochemical production includes enzymatic synthesis/decomposition and genetic engineering synthesis (host cells may be either prokaryotic cells such as bacteria, or eukaryotic cells such as yeasts or animal cells) (the same applies to the following other components).
  • host cells may be either prokaryotic cells such as bacteria, or eukaryotic cells such as yeasts or animal cells) (the same applies to the following other components).
  • the antibody upper hinge region-forming sequence Z U may be either a biological sequence or a non-biological sequence, and may be obtained by any method which is well-known to those skilled in the art such as isolation from a natural product, organic chemical synthesis, biochemical production, or semisynthesis.
  • a method which is well-known to those skilled in the art can be performed for obtaining the molecular recognition system-forming substance X and the antibody upper hinge region-forming sequence Z U in a state where these components are linked together via the alkyleneoxide-containing group Y.
  • the thioester group can be appropriately derived from the C-terminal carboxyl group of the antibody upper hinge region-forming sequence by those skilled in the art.
  • an antibody Fc fragment-containing peptide having an antibody Fc fragment and an N-terminal cysteine residue is prepared.
  • the antibody Fc fragment-containing peptide may have an amino acid residue or a peptide chain L between the N-terminal cysteine residue and the Fc fragment [represented by Cys-L-Fc (L is an amino acid residue or a peptide chain)].
  • the antibody Fc fragment-containing peptide preferably has at least one another cysteine residue between the cysteine residue and the antibody Fc fragment [e.g., represented by Cys-L 1 -Cys-L 2 -Fc (L 1 and L 2 are an amino acid residue or a peptide chain)].
  • the antibody Fc fragment-containing peptide contains an antibody core hinge region-forming sequence Z C
  • the N-terminal cysteine residue corresponds to an N-terminal cysteine residue of the antibody core hinge region-forming sequence Z C
  • the above-described at least one another cysteine residue is also contained in the antibody core hinge region-forming sequence Z C [e.g., represented by Cys-L 1 -Cys-L 2 -Fc (Cys-L 1 -Cys is the antibody core hinge region-forming sequence Z C )].
  • the antibody Fc fragment-containing peptide may further contain an antibody lower hinge region-forming sequence ZL [e.g., represented by Cys-L 1 -Cys-L 2 -Fc (L 2 is the antibody lower hinge region-forming sequence Z L )].
  • ZL an antibody lower hinge region-forming sequence
  • the antibody Fc fragment-containing peptide can be obtained by a peptide production method which is well-known to those skilled in the art. Therefore, the antibody Fc fragment-containing peptide may be obtained by any method which is well-known to those skilled in the art such as isolation from a natural product, organic chemical synthesis, biochemical production, semisynthesis, and the like, or a combination of two or more of them.
  • the nonpeptide hinge part-containing thioester (XYZ U -COSR) and the antibody Fc fragment-containing peptide (e.g., Cys-L-Fc) are brought into contact with each other so that a native chemical ligation reaction occurs.
  • the reaction can be performed by incubation in a buffer solution under non-heating conditions (room temperature) for 6 to 16 hours.
  • a buffer solution under non-heating conditions (room temperature) for 6 to 16 hours.
  • an antibody-like molecule having the XYZ U -group and the antibody Fc fragment, to which the XYZ U -group is bound via the cysteine residue e.g., XYZ U -Cys-Z-Fc
  • Fig. 1 illustrates the mechanism of the native chemical ligation with reference to one example of the present invention.
  • Fig. 1 illustrates a case where the nonpeptide hinge part-containing thioester contains amyloid ⁇ (1-15) DAEFRHDSGYEVHHQ (SEQ ID No. 2) as the molecular recognition system-forming substance X, polyethyleneglycol with a polymerization degree of x (PEG) x as the alkyleneoxide-containing group Y, and DKTHT (SEQ ID No. 1) as the antibody upper hinge region-forming sequence Z U ; and the antibody Fc fragment-containing peptide is a peptide having CPPC (SEQ ID No. 5) as the antibody core hinge region-forming sequence Z C and PAELLGGP (SEQ ID No. 6) as the antibody lower hinge region-forming sequence Z L .
  • DAEFRHDSGYEVHHQ SEQ ID No. 2
  • PEG polyethyleneglycol with a polymerization degree of x
  • DKTHT S
  • an S-acyl intermediate is reversibly formed by transthioesterification ( Fig. 1A ), the S-acyl intermediate undergoes spontaneous S- to N-acyl migration ( Fig. 1B ), and a peptide bond is irreversibly formed via a five-membered ring intermediate ( Fig. 1C ).
  • Fc6 A recombinant Fc protein (called Fc6) was expressed in Chinese hamster ovary (CHO) cells and purified by Protein A affinity chromatography.
  • a DNA expression vector was designed that directs the expression of a chimeric protein containing a human sonic hedgehog homolog (SHH) signal sequence fused to a human IgG1 heavy chain hinge region beginning at a 226 CPPC core hinge sequence (heavy chain residues are numbered according to the Eu format 3) ; residue 226 Cys corresponds to Cys239 in kobat & Wu format) 24) .
  • SHH human sonic hedgehog homolog
  • the crude protected peptide was treated with DIC/HOBt/DIEA and either thiophenol (Peptides 1, 2, 5) or benzyl mercaptan (Peptides 3, 4) in DCM overnight to form a thioester of the peptide. After concentration, the crude protected peptide thioester was precipitated by multiple triturations with cold ether, followed by centrifugation. Deprotection was carried out by treatment of the crude protected product with 95 : 2.5 : 2.5 TFA/TIS/H 2 O (volume ratio) at room temperature for 2 hours.
  • the deprotected peptide thioester was purified by preparative RP-HPLC in a H 2 O-acetonitrile (0.1 vol% TFA) system to obtain a final product with a purity of 91-95% and a desired MS.
  • MES 2-(N-morpholino)ethanesulfonicacid
  • TCEP tris(2-carboxyethyl)phosphine
  • MPAA 4-mercaptophenylacetic acid
  • reaction products were analyzed by SDS polyacrylamide gel electrophoresis (SDS-PAGE) under reducing conditions using NuPAGE (registered trademark) Novex Bis-Tris Midi Gels (10%) purchased from Invitrogen (Carlsbad, CA). Proteins were visualized using Silver Stain Plus or Coomassie Brilliant Blue R-250 purchased from Bio-Rad (Hercules, CA).
  • HPLC-grade acetonitrile (ACN) and trifluoroacetic acid (TFA) were purchased from Wako Pure Chemical Industries (Osaka, Japan) .
  • Ammonium bicarbonate (NH 4 HCO 3 ), dithiotreitol (DTT), and iodoacetamide (IAA) were purchased from Nacalai Tesque (Kyoto, Japan).
  • Sequence grade trypsin was purchased from Promega (Madison, WI) . Protein bands from the gel were excised and destained with 300 ⁇ l of a solution containing 50% v/v ACN in an aqueous 50 mM NH 4 HCO 3 solution at 4°C for 45 minutes.
  • the gel pieces were dehydrated in 150 ⁇ l of 100% ACN at room temperature for 10 minutes and then dried using Speed Vac (registered trademark) for 30 minutes.
  • the proteins were alkylated in 100 ⁇ l of a solution containing 55 mM IAA in an aqueous 50 mM NH 4 HCO 3 solution at room temperature for 1 hour under the dark.
  • the gel pieces were washed with 150 ⁇ l of an aqueous 50 mM NH 4 HCO 3 solution and then dehydrated in 150 ⁇ l of 100% ACN. This step was repeated 2 times.
  • the gel pieces were then dried in a vacuum centrifuge for 30 minutes.
  • the dried gels were rehydrated with 2 ⁇ l of a solution containing 50 ng/ ⁇ l of trypsin in an aqueous 50 mM NH 4 HCO 3 solution, and incubated at room temperature for 5 minutes. Then, 18 ⁇ l of ultrapure water was further added, and the proteins were digested at 37°C overnight.
  • MALDI mass spectra were obtained using AXIMA performance MALDI-TOF mass spectrometer (Shimadzu/KRATOS, Manchester, UK) equipped with a 337 nm nitrogen laser in the positive ion reflectron mode and the linear mode.
  • ⁇ -Cyano-4-hydroxy-cinnamic acid (CHCA) and sinapinic acid (SA) were obtained from LaserBio Labs (Sophia-Antipolis Cedex, France).
  • CHCA was used for trypsin-digested proteins
  • SA was used for SEC-separated proteins.
  • a matrix solution was prepared by dissolving 5 mg of the matrix compound in 0.5 ml of an aqueous 50% v/v ACN solution containing 0.1% v/v TFA.
  • a sample solution (0.5 ⁇ l) was mixed with an equivalent amount of the matrix solution on a target plate and then dried at room temperature for MALDI-TOF MS analysis.
  • the m/z values were calibrated using, as external standard, 2 pmol of each of [Angiotensin I + H + ] (m/z 1296.7), [Angiotensin II + H + ] (m/z 1046.5), [[Glu1]-Fibrinopeptide B + H + ] (m/z 1570.7), [N-acetyl-resin substrate tetradecapeptide I + H + ] (m/z 1800.9), [ACTH fragment 1-17 + H + ] (m/z 2093.1) and [ACTH fragment 18-39 + H + ] (m/z 2464.2), and 3 pmol of [ACTH fragment 7-38 + H + ] (m/z 3656.9), 7.5 pmol of [Bovine serum albumin + H + ] (m/z 66430.09 (average)), and [Aldolase + H + ] (m/z 39212.28 (average)).
  • reaction products purified with Protein A were first concentrated 10-fold using 0.5 ml Amicon Ultracel-3K centrifugal filters (Millipore, Cork, IR); 50 ⁇ l of each concentrate was then applied to four TSKgel columns coupled in series (two G2000SW XL and two G3000SW XL [7.8 mm I.D.
  • Binding of A ⁇ symmetroadhesins and A ⁇ peptides was carried out at 25°C in 10 mM Hepes buffer, pH 7.4, 150 mM NaCl, 3 mM EDTA, and 0.005 vol% Tween-20. Data was evaluated using Biacore T100 Evaluation Software, version 2.0.3.
  • FIG. 1 A strategy of the present inventors for chemical semisynthesis of A ⁇ symmetroadhesin is shown in Fig. 1 .
  • a native chemical ligation was carried out using the recombinant Fc protein (Fc6) engineered to have cysteine residues at both N-termini.
  • Fc6 the recombinant Fc protein
  • the present inventors developed mildly reducing, non-denaturing conditions that favor a stable Fc dimer and maintain the sulfhydryl groups of the N-terminal cysteines in a reduced state, allowing the Fc6 molecule to readily react with C-terminal thioesters.
  • Nucleophilic acyl substitution involving both the N-terminal sulfhydryls of the Fc6 molecule as nucleophiles ( Fig. 1A ) leads to a thioester-linked intermediate having two A ⁇ thioesters ( Fig. 1B ).
  • Subsequent nucleophilic attack by both the Fc6 N-terminal amino groups followed by intramolecular rearrangement results in irreversible peptide bond formation between Fc6 and two A ⁇
  • the present inventors employed a recombinant DNA construct placed a signal sequence placed adjacent to a cysteine residue normally found in the hinge region.
  • the IgG1 hinge region contains three cysteine residues, i.e., 220 Cys in the upper hinge region (CDKTHT (SEQ ID No. 8)) which usually participates in the disulfide bond between the heavy chain and the light chain; and 226 Cys and 229 Cys in the core hinge region (CPPC (SEQ ID No. 5)) which are sometimes present in the interchain disulfide bonds between two heavy chains.
  • CDKTHT SEQ ID No. 8
  • 226 Cys and 229 Cys in the core hinge region CPPC (SEQ ID No. 5)
  • the present inventors selected 226 Cys over 220 Cys as the N-terminus for the Fc molecules of the present inventors.
  • the signal sequence of the sonic hedgehog homolog (SHH) was chosen for the secretion and processing of the Fc protein since its own mature polypeptide has an N-terminal cysteine.
  • the pCDNA3-SHH-TgG1-Fc11 construct efficiently directed the synthesis of the Fc6 protein following the transient transfection of Chinese hamster ovary (CHO) cells.
  • Fig. 2 shows that the Fc6 product obtained by the affinity purification of the transfected CHO cell supernatants has an apparent molecular weight of 27,000 daltons on SDS-PAGE under reducing conditions (lane 1).
  • the Fc6 protein was well expressed in transient transfections and reached levels exceeding 0.8 g/L, and was found to quantitatively bind and elute from Protein A affinity resins.
  • Fc6 Fc6 to react with five different C-terminal thioesters (listed in Table 1) was investigated. All the five thioesters contain a portion of the upper hinge region (DKTHT (SEQ ID No. 1)) at their C-terminus. Four of the five thioesters also contain 15 amino acid sequence (DAEFRHDSGYEVHHQ (SEQ ID No. 2)) derived from a human A ⁇ protein bound at C-terminus to the N-terminus of the upper hinge region. In addition, three of the A ⁇ -containing thioesters incorporated a nonpeptide chain between the A ⁇ sequence and the upper hinge sequence. The nonpeptide portions in these peptides were composed of oxyethylene oligomer (PEG) of a chain length of 12, 24, or 36, respectively.
  • PEG oxyethylene oligomer
  • Fig. 2 shows that Fc6 reacted quantitatively with all the five thioesters, so that a ladder of products of increasing size was yielded on SDS-PAGE under reducing conditions (lanes 2-6). Similar to the 15 amino acid residue A ⁇ sequence, the addition of the PEG 12 oligomer gave a size increase on SDS-PAGE (compare lanes 2-4 in Fig. 2 ). This suggests that a single amino acid residue and a single oxyethylene monomer unit make similar contributions to contour length, while being consistent with the comparable lengths of their transconformations (approximately 3.5 to 4 angstroms) 16) . The addition of PEG 24 and PEG 36 gave further size increases over PEG 12 , and the increases were consistent (compare lanes 3-6 in Fig. 2 ).
  • Fc6 As a native, folded protein by secretion in mammalian cells, it was critically important to avoid the use of chaotropic agents and strong reducing conditions typically employed in other native chemical ligation studies 17) . Nevertheless, mild reducing conditions were essential. The reason for this is that, otherwise, the Fc6 protein was found to be essentially unreactive with thioesters (data not shown). The quantitative yields of symmetroadhesins (>90%) were readily obtained as seen in Fig. 2 by combining a non-thiol reducing agent such as tris (2-carboxyethyl) phosphine with a thiol reducing agent such as 4-mercaptophenylacetic acid 26) .
  • a non-thiol reducing agent such as tris (2-carboxyethyl) phosphine
  • a thiol reducing agent such as 4-mercaptophenylacetic acid 26
  • the present inventors analyzed the monomer structures of the four A ⁇ symmetroadhesins by mass spectrometry.
  • the A ⁇ -Fc, A ⁇ -PEG 12 -Fc, A ⁇ -PEG 24 -Fc, and A ⁇ -PEG 36 -Fc symmetroadhesin reaction products were purified by SDS-PAGE and characterized using in-gel tryptic digestion. Peaks detected by MALDI-TOF MS were fit to theoretical peptides predicted for symmetroadhesins, respectively, so that a sequence coverage between 78.9-81.8% was obtained ( Figs.
  • the A ⁇ symmetroadhesin reaction products were expected to have a dimeric structure similar to that of the parent Fc6 molecule.
  • each of the reaction products may be a mixture of homodimers having two A ⁇ "hands", heterodimers having one A ⁇ "hand”, and unreacted Fc6 homodimers. Accordingly, size exclusion chromatography (SEC) was used in order to investigate the subunit molecular structures of the four A ⁇ symmetroadhesins.
  • the A ⁇ -Fc, A ⁇ -PEG 12 -Fc, A ⁇ -PEG 24 Fc and A ⁇ -PEG 36 -Fc reaction products were purified from unreacted thioester by Protein A affinity chromatography, and then analyzed by SEC under native, non-reducing conditions (50 mM sodium phosphate, pH 7.4, 300 mM NaCl).
  • Figs. 6A, 6B , 7A, and 7B show that all the four symmetroadhesin reaction products exhibited two main peaks. The sizes of these two main peaks increased in the order A ⁇ -Fc ⁇ A ⁇ -PEG 12 -Fc ⁇ A ⁇ -PEG 24 -Fc ⁇ A ⁇ -PEG 36 -Fc.
  • Table 2 shows A ⁇ -PEG x -Fc symmetroadhesin product ratios determined by size exclusion chromatography (SEC). The ratios for each of the four reaction (Reaction) products shown in Figs. 3 and 4 were calculated directly from the area of each peak. HMW represents a molecular species having a higher molecular weight, and ND represents not detected.
  • MW (observed) 1 represents the molecular weight of each of the two-handed and one-handed products in each of the four reactions (Reaction) shown in Figs. 6 and 7
  • ⁇ MW 2 represents the difference in molecular weight between the two-handed and one-handed products in each of the reactions (Reaction).
  • the present inventors characterized the binding of the A ⁇ symmetroadhesins of the present inventors to one of these antibodies (6E10) using surface plasmon resonance (SPR).
  • SPR surface plasmon resonance
  • the present inventors compared the binding of A ⁇ peptides containing the DAEFRHDSGYEVHHQ sequence (SEQ ID No. 2) which were expected to bind to 6E10 in a one-handed manner.
  • FIGS. 12 to 14 show the results obtained when 6E10 was immobilized on the surface of the SPR chip. Specific binding was observed with all the four A ⁇ symmetroadhesins ( Figs. 12A, 12B , 13A, and 13B) and with two A ⁇ peptides, i.e., pen-A ⁇ and A ⁇ -pra (Table 1) ( Figs. 14E and 14F ), that contained the 15 amino acid A ⁇ sequence. No binding was observed at all with Fc6 or the DKTHT-Fc6 symmetroadhesin ( Fig. 2 , lane 2), and accordingly it was confirmed that binding was specific for the A ⁇ sequence.
  • Table 4 shows the kinetic results of Mab-6E10 binding measured by surface plasmon resonance.
  • the kinetic binding curves for both of the A ⁇ peptides gave a good fit with a 1:1 Langmuir model (x 2 ⁇ 0.1), which was consistent with one-handed binding.
  • the four A ⁇ symmetroadhesins did not give a good fit with the 1:1 Langmuir model (x 2 > 10), and this indicated two classes of binding sites.
  • a good fit was obtained for the four A ⁇ symmetroadhesins by employing a two-exponential model (x 2 ⁇ 1.1).
  • the single affinity site exhibited by the pen-A ⁇ (17 nM) and A ⁇ -pra (20 nM) peptides was similar to the low affinity sites observed for the A ⁇ -Fc (140 nM), A ⁇ -PEG 12 -Fc (93 nM), A ⁇ -PEG 24 -Fc (70 nM), and A ⁇ -PEG 36 -Fc (62 nM) symmetroadhesins (Table 4) .
  • This low affinity site was consistent with a one-handed binding mechanism by a fraction of the symmetroadhesin population.
  • Proteins prefer to form compact globular or fibrous structures, so that their exposure to solvent is minimized. This tendency is inherent both in the polypeptide backbone having a propensity for hydrogen-bound secondary structure, and in side chain interactions that promote tertiary folding. Therefore, most of previous efforts to introduce "flexibility" into antibodies using peptides have been inadequate. For example, it is common to employ a combination of an amino acid that favors solvent interactions (e.g., serine) and an amino acid that breaks a helical structure (e.g., glycine). This approach is useful in making fusion proteins such as single-chain antibody fragments (scFv), but the resulting structures are quite compact with no evidence of extendibility (for example, see Reference Document 20). Further, such sequences are likely to cause additional problems due to their intrinsic immunogenicity and proteolytic susceptibility.
  • an amino acid that favors solvent interactions e.g., serine
  • an amino acid that breaks a helical structure e.g., glycine
  • the present inventors pursued a novel strategy that introduces a nonprotein chain into the hinge region by chemical semisynthesis.
  • the results of the present inventors demonstrate quantitative yields of antibody-like molecules having nonprotein hinge parts that connect the two A ⁇ 1-15 peptides with the Fc dimer. These molecules form two-handed native dimers that exhibit high affinity for an anti-A ⁇ monoclonal antibody.
  • the A ⁇ -PEG x -Fc dimer having a nonprotein hinge part of the present inventors has an affinity that is two to five orders of magnitude greater than the cognate peptide, and is therefore considered to bind much better than the A ⁇ -Fc dimer.
  • the analysis by SDS-polyacrylamide gel electrophoresis indicates that the formation of the desired A ⁇ -PEG x -Fc fusion protein exceeds 90%.
  • the MS analysis of the one-handed reaction products purified by SEC indicates that they contain two reacted Fc polypeptides ( Fig. 11 ), one of which is full-length but the other of which has been hydrolyzed at the T/HT sequence that is a major site of proteolysis (e.g., papain) 9) . Therefore, the overall efficiency of the native chemical ligation step, excluding the subsequent cleavage, may be much closer to 100%.
  • the native ligation conditions also appear to be completely compatible with the native structure and bioactivity of the Fc dimer, while imparting some of the properties of nonprotein polymers.
  • the results of the present inventors indicate that the addition of discrete oxyethylene oligomers not only improves binding but also appears to have a significant effect on the hydrodynamic radius of the Fc protein as evidenced by the size exclusion chromatography of the A ⁇ -PEG 12 -Fc, A ⁇ -PEG 24 Fc, and A ⁇ -PEG 36 -Fc molecules when compared with the A ⁇ -Fc molecule.
  • MALDI-TOF MS appears to be ideally suited for the characterization of the novel protein-nonprotein-protein molecules of the present inventors.
  • the most part contributed by the hybrid structures can be efficiently characterized not only in tryptic digests, but also in the two-handed and one-handed native Fc dimers. Ionization and desorption appear to be mediated by the adjacent protein sequences in the protein-nonprotein hybrid molecules of the present inventors, and this suggest the application of this approach to a broad range of chemically distinct polymer chains.
  • the present inventors have described here a significant step toward the goal of the present inventors, i.e. , toward the complete chemical semisynthesis of antibodies having nonprotein hinge parts that incorporate large binding domains such as the Fab region itself or receptor extracellular domains. Additional progress will depend upon the identification of other protein ligation reactions that can be combined with a native chemical ligation; that are similarly compatible with the native structure and function of the cognate proteins; and that can efficiently proceed at micromolar concentrations that are achievable using such native proteins in solution.
  • the antibody-like molecule that is envisioned by the present inventors has enormous potential as a candidate therapeutic agent having improved binding affinity for disease targets.

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